Establishing chemical design rules that simultaneously control the electronic structure and thermal transport is a long-sought goal for heat-management and energy materials. Here, we demonstrate that a single B-to-C substitution changes the electron count and simultaneously reconstructs the bonding network and crystal structure, driving a metal-to-semiconductor transition while concurrently enhancing the lattice thermal conductivity. Using density-functional theory (DFT) and machine-learned interatomic potentials (MLIPs), we investigate the electronic structure, lattice dynamics, and phonon thermal transport in cubic BaB3C3 and its B-to-C-substituted tetragonal BaB2C4 structure. The substitution donates one electron per formula unit to the B-C framework, thereby triggering the formation of strong C-C bonds and opening a bandgap of 0.33 eV. The Message Passing Atomic Cluster Expansion (MACE) model reproduces DFT energies and forces, yielding phonon dispersion and lattice thermal conductivity in excellent agreement with DFT benchmarks. Thermodynamically stable cubic BaB3C3 possesses an isotropic lattice thermal conductivity of 7.6 W/mK at 300 K. Substituting B with C hardens the phonon dispersion (evidenced by a frequency upshift from ~800 to ~900 cm^-1) and simultaneously boosts both phonon group velocities and lifetimes. Consequently, the lattice thermal conductivity surges to 18.7 W/mK, representing a remarkable ~2.5-fold enhancement of the in-plane component and a transformation from isotropic to anisotropic behavior, characterized by kappa_x = kappa_y > kappa_z. Our results demonstrate that minimal B-to-C substitution provides a viable strategy to modulate the electronic structure, thereby transforming the crystal from a metal to a semiconductor and concomitantly enhancing phonon thermal transport.